Abstract
Enterobacteria belonging to the Pectobacterium and Dickeya genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as Pectobacterium punjabense, are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of P. punjabense. All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of P. punjabense strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of P. punjabense species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.
Highlights
Introduction published maps and institutional affilBacteria belonging to the Pectobacterium and Dickeya genera are causal agents of soft rots in a wide variety of host plants [1]
The genetic diversity and phenotypic variation of Pectobacterium punjabense in Europe by the analysis of strains deposited in culture collections
The Multi-Locus Sequence Analysis (MLSA) phylogenic tree including strains tentatively identified as P. punjabense derived from European collections and type strains from phylogenetically related Pectobacterium species was built from the concatenated sequences of fourteen housekeeping genes extracted from genomes
Summary
Introduction published maps and institutional affilBacteria belonging to the Pectobacterium and Dickeya genera are causal agents of soft rots in a wide variety of host plants [1]. The agricultural and economic impact ranks these pathogens classified within the group of soft rot Pectobacteriaceae (SRP) [2] among the most studied phytopathogenic bacteria [3]. They produce extracellular enzymes degrading plant cell walls [4,5] causing the breakdown of plant tissues. The losses can be significant [7] and, to date, chemical, physical or biocontrol applications have shown limited efficacy. Prophylactic methods such seed sanitation and breeding potato cultivars to improve natural resistance are still highly recommended [8]
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